Ghaffarian Sara, Panahi Bahman
Department of Cellular and Molecular Biology, Faculty of Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran.
Department of Genomics, Branch for Northwest & West region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.
Front Microbiol. 2024 Jul 11;15:1357156. doi: 10.3389/fmicb.2024.1357156. eCollection 2024.
The genus is primarily known for its significance in acetic acid production and its application in various industrial processes. This study aimed to shed light on the prevalence, diversity, and functional implications of CRISPR-Cas systems in the genus using a genome mining approach. The investigation analyzed the CRISPR-Cas architectures and components of 34 Acetobacter species, as well as the evolutionary strategies employed by these bacteria in response to phage invasion and foreign DNA. Furthermore, phylogenetic analysis based on CAS1 protein sequences was performed to gain insights into the evolutionary relationships among Acetobacter strains, with an emphasis on the potential of this protein for genotyping purposes. The results showed that 15 species had orphan, while20 species had complete CRISPR-Cas systems, resulting in an occurrence rate of 38% for complete systems in Acetobacter strains. The predicted complete CRISPR-Cas systems were categorized into I-C, I-F, I-E, and II-C subtypes, with subtype I-E being the most prevalent in Acetobacter. Additionally, spacer homology analysis revealed against such the dynamic interaction between Acetobacter strains and foreign invasive DNAs, emphasizing the pivotal role of CRISPR-Cas systems in defending against such invasions. Furthermore, the investigation of the secondary structures of CRISPR arrays revealed the conserved patterns within subtypes despite variations in repeat sequences. The exploration of protospacer adjacent motifs (PAMs) identified distinct recognition motifs in the flanking regions of protospacers. In conclusion, this research not only contributes to the growing body of knowledge on CRISPR-Cas systems but also establishes a foundation for future studies on the adaptive defense mechanisms of Acetobacter. The findings provide valuable insights into the intricate interplay between bacteria and phages, with implications for industrial applications and potential biotechnological advancements.
该属主要因其在乙酸生产中的重要性及其在各种工业过程中的应用而闻名。本研究旨在通过基因组挖掘方法，揭示该属中CRISPR-Cas系统的流行情况、多样性及其功能意义。该调查分析了34种醋杆菌属物种的CRISPR-Cas结构和组成部分，以及这些细菌应对噬菌体入侵和外源DNA所采用的进化策略。此外，基于CAS1蛋白序列进行了系统发育分析，以深入了解醋杆菌菌株之间的进化关系，重点是该蛋白用于基因分型的潜力。结果表明，15个物种有孤儿CRISPR-Cas系统，而20个物种有完整的CRISPR-Cas系统，醋杆菌菌株中完整系统的发生率为38%。预测的完整CRISPR-Cas系统分为I-C、I-F、I-E和II-C亚型，其中I-E亚型在醋杆菌属中最为普遍。此外，间隔区同源性分析揭示了醋杆菌菌株与外源入侵DNA之间的动态相互作用，强调了CRISPR-Cas系统在抵御此类入侵中的关键作用。此外，对CRISPR阵列二级结构的研究揭示了尽管重复序列存在差异，但各亚型内的保守模式。对原间隔相邻基序（PAM）的探索在原间隔侧翼区域鉴定出不同的识别基序。总之，本研究不仅为关于CRISPR-Cas系统的知识增长做出了贡献，也为未来关于醋杆菌适应性防御机制的研究奠定了基础。这些发现为细菌与噬菌体之间的复杂相互作用提供了有价值的见解，对工业应用和潜在的生物技术进步具有启示意义。
